In vitro: Natural Compounds (Thymol, Carvacrol, Hesperidine, And Thymoquinone) Against Sars-Cov2 Strain Isolated From Egyptian Patients

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   ScreenIT

   Nov 9, 2020

   SciScore for 10.1101/2020.11.07.367649: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   B) Plaque reduction assay: Assay was carried out according to the method of 37 in a six well plate where Vero E6 cells (105 cells / ml) were cultivated for 24 hrs at 37°C.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   In silico testing: Before performing the docking studies, the tested compounds are retrieved from the PubChem database and then prepared using PyMOL software 22,23.	PubChem suggested: (PubChem, RRID:SCR_0042…

   SciScore for 10.1101/2020.11.07.367649: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   B) Plaque reduction assay: Assay was carried out according to the method of 37 in a six well plate where Vero E6 cells (105 cells / ml) were cultivated for 24 hrs at 37°C.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   In silico testing: Before performing the docking studies, the tested compounds are retrieved from the PubChem database and then prepared using PyMOL software 22,23.	PubChem suggested: (PubChem, RRID:SCR_004284)
   The docking experiments are performed utilizing Autodock Vina software in triplicates to have a clear depiction of the mode of action of compounds against their protein targets 26.	Autodock Vina suggested: (AutoDock Vina, RRID:SCR_011958)
   PyMOL software was used to represent and analyze the docking complexes.	PyMOL suggested: (PyMOL, RRID:SCR_000305)
   Statistical analysis: Analysis was performed using Graphpad Prism 8.0.2.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 8. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Read the original source
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   Version published to 10.1101/2020.11.07.367649 on bioRxiv

   Nov 8, 2020